Is NUS1 p.Phe30= (c.90C>T) pathogenic?

NUS1 p.Phe30= (c.90C>T) is classified Likely benign in NUS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-14). Ultra-rare (popmax 0.0333%, eas); Associated with congenital disorder of glycosylation, type Iaa.

What condition is associated with NUS1 p.Phe30= (c.90C>T)?

NUS1 p.Phe30= (c.90C>T) is associated with congenital disorder of glycosylation, type Iaa (ClinVar).

How common is NUS1 p.Phe30= (c.90C>T) in the general population?

NUS1 p.Phe30= (c.90C>T) is ultra-rare (popmax 0.0333%, eas) (gnomAD).

NUS1 p.Phe30=

c.90C>T · rs1456601831 · VCV2185755

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0333%, eas)

Conditions

congenital disorder of glycosylation, type Iaa

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.53 · evaluated, not missing
Constraint at this position
Conservation	phyloP 1.2	GERP 1.8, phastCons 1
Overall
CADD	13.16	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0333% East Asian · 14/42,020 alleles

Filtering AF 0.02% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0161%

Overall 0.000965% 15/1,554,998 alleles · ultra-rare exomes 12/1,403,034 · genomes 3/151,964 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0333%	3,001
European (non-Finnish)	8.66e-05%	1,154,188

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: NUS1
Protein: p.Phe30=
Coding: c.90C>T
MANE Select: NM_138459
dbSNP: rs1456601831
Type: single nucleotide variant
Location: chr6:117675760 (GRCh38)
Gene constraint: LOEUF 0.182 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 82.01 · 9 PDB

Full NUS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

congenital disorder of glycosylation, type Iaa — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

NUS1 p.Phe30Cys Uncertain significance ★ ⚠ same residue
NUS1 c.415+1G>A Pathogenic/Likely pathogenic ★★ same condition
NUS1 c.692-2A>G Likely pathogenic ★★ same condition
NUS1 p.Arg290Cys Pathogenic/Likely pathogenic ★★ same condition
NUS1 p.Leu240Ter Pathogenic/Likely pathogenic ★★ same condition
NUS1 p.Ala44Thr Uncertain significance ★★ ⚠ same condition
NUS1 p.Ala79Val Uncertain significance ★★ ⚠ same condition
NUS1 p.Arg10Trp Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/nus1-p-phe30 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown